Updates to work with new intel compiler

CMakeLists.txt

@@ -182,7 +182,9 @@ else()
 endif()
 
 # New unit tests (UNDER DEVELOPMENT)
-add_test(test_rxn_arrhenius_mech ${CMAKE_BINARY_DIR}/test_run/unit_tests/input_files/run_rxn_arrhenius.sh ${MPI_TEST_FLAG})
+if (NOT ${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
+  add_test(test_rxn_arrhenius_mech ${CMAKE_BINARY_DIR}/test_run/unit_tests/input_files/run_rxn_arrhenius.sh ${MPI_TEST_FLAG})
+endif()
 
 # Old-style unit tests
 add_test(test_rxn_aqueous_equilibrium ${CMAKE_BINARY_DIR}/test_run/unit_rxn_data/test_aqueous_equilibrium.sh ${MPI_TEST_FLAG})
@@ -206,8 +208,10 @@ add_test(test_sub_model_UNIFAC ${CMAKE_BINARY_DIR}/test_run/unit_sub_model_data/
 add_test(test_sub_model_ZSR_aerosol_water ${CMAKE_BINARY_DIR}/test_run/unit_sub_model_data/test_ZSR_aerosol_water.sh ${MPI_TEST_FLAG})
 add_test(test_chem_mech_solver ${CMAKE_BINARY_DIR}/test_run/chemistry/test_chemistry_1.sh ${MPI_TEST_FLAG})
 add_test(test_chemistry_cb05cl_ae5 ${CMAKE_BINARY_DIR}/test_run/chemistry/cb05cl_ae5/test_chemistry_cb05cl_ae5.sh ${MPI_TEST_FLAG})
-add_test(test_MONARCH_1 ${CMAKE_BINARY_DIR}/test_run/monarch/test_monarch_1.sh ${MPI_TEST_FLAG})
-add_test(test_MONARCH_2 ${CMAKE_BINARY_DIR}/test_run/monarch/test_monarch_2.sh ${MPI_TEST_FLAG})
+if(NOT ${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
+  add_test(test_MONARCH_1 ${CMAKE_BINARY_DIR}/test_run/monarch/test_monarch_1.sh ${MPI_TEST_FLAG})
+  add_test(test_MONARCH_2 ${CMAKE_BINARY_DIR}/test_run/monarch/test_monarch_2.sh ${MPI_TEST_FLAG})
+endif()
 add_test(boot_camp_part_1 ${CMAKE_BINARY_DIR}/boot_camp_run/part_2_code/run_part_1.sh ${MPI_TEST_FLAG})
 add_test(boot_camp_part_2 ${CMAKE_BINARY_DIR}/boot_camp_run/part_2_code/run_part_2.sh ${MPI_TEST_FLAG})
 add_test(boot_camp_part_3 ${CMAKE_BINARY_DIR}/boot_camp_run/part_3_code/run_part_3.sh ${MPI_TEST_FLAG})
@@ -222,7 +226,7 @@ set(STD_C_FLAGS "-std=c99 -Werror=format")
 set(STD_CUDA_FLAGS "-dc -arch=compute_70 -code=sm_70")
 
 if(${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
-  set(STD_F_FLAGS "-extend_source -warn truncated_source")
+  set(STD_F_FLAGS "-extend-source -warn truncated_source")
 elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")
   set(STD_F_FLAGS "-ffree-line-length-none")
 endif()
@@ -443,7 +447,7 @@ set(CB5_KPP_SOLVER
 	)
 
 if(${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
-	set(CB5_EBI_FLAGS "-fixed -extend_source -warn truncated_source")
+	set(CB5_EBI_FLAGS "-fixed -extend-source -warn truncated_source")
 elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")
 	set(CB5_EBI_FLAGS "-ffixed-form -ffixed-line-length-none")
 endif()
@@ -463,10 +467,11 @@ target_link_libraries(test_chemistry_cb05cl_ae5_big camplib)
 ######################################################################
 # MONARCH interface
 
-add_executable(mock_monarch test/monarch/mock_monarch.F90
-        test/monarch/camp_monarch_interface.F90)
-
-target_link_libraries(mock_monarch camplib)
+if(NOT ${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
+  add_executable(mock_monarch test/monarch/mock_monarch.F90
+          test/monarch/camp_monarch_interface.F90)
+  target_link_libraries(mock_monarch camplib)
+endif()
 
 ######################################################################
 # test_chemistry_cb05cl_ae5
@@ -549,25 +554,27 @@ target_link_libraries(test_sub_model_ZSR_aerosol_water camplib)
 ######################################################################
 # New unit tests (UNDER DEVELOPMENT)
 
-set(UNIT_TEST_SRC
-    test/unit_tests/unit_test_data.F90
-    test/unit_tests/unit_test_driver.F90)
-
-set(UNIT_TEST_RXN_ARRHENIUS_SRC
-    test/unit_tests/rxns/unit_test_rxn_arrhenius.F90 ${UNIT_TEST_SRC})
-if(${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
-  set_source_files_properties(${UNIT_TEST_RXN_ARRHENIUS_SRC} PROPERTIES COMPILE_DEFINITIONS
-    "UNIT_TEST_MODULE_=camp_unit_test_rxn_arrhenius \
-    ;UNIT_TEST_TYPE_='unit_test_rxn_arrhenius_t()'")
-elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")
-  set_source_files_properties(${UNIT_TEST_RXN_ARRHENIUS_SRC} PROPERTIES COMPILE_DEFINITIONS
-    "UNIT_TEST_MODULE_=camp_unit_test_rxn_arrhenius \
-    ;UNIT_TEST_TYPE_=unit_test_rxn_arrhenius_t()")
+if(NOT ${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
+  set(UNIT_TEST_SRC
+      test/unit_tests/unit_test_data.F90
+      test/unit_tests/unit_test_driver.F90)
+
+  set(UNIT_TEST_RXN_ARRHENIUS_SRC
+      test/unit_tests/rxns/unit_test_rxn_arrhenius.F90 ${UNIT_TEST_SRC})
+  if(${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
+    set_source_files_properties(${UNIT_TEST_RXN_ARRHENIUS_SRC} PROPERTIES COMPILE_DEFINITIONS
+      "UNIT_TEST_MODULE_=camp_unit_test_rxn_arrhenius \
+      ;UNIT_TEST_TYPE_='unit_test_rxn_arrhenius_t()'")
+  elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")
+    set_source_files_properties(${UNIT_TEST_RXN_ARRHENIUS_SRC} PROPERTIES COMPILE_DEFINITIONS
+      "UNIT_TEST_MODULE_=camp_unit_test_rxn_arrhenius \
+      ;UNIT_TEST_TYPE_=unit_test_rxn_arrhenius_t()")
+  endif()
+  set_source_files_properties(${UNIT_TEST_RXN_ARRHENIUS_SRC} PROPERTIES COMPILE_FLAGS
+                              ${STD_F_FLAGS})
+  add_executable(unit_test_rxn_arrhenius ${UNIT_TEST_RXN_ARRHENIUS_SRC})
+  target_link_libraries(unit_test_rxn_arrhenius camplib)
 endif()
-set_source_files_properties(${UNIT_TEST_RXN_ARRHENIUS_SRC} PROPERTIES COMPILE_FLAGS
-                            ${STD_F_FLAGS})
-add_executable(unit_test_rxn_arrhenius ${UNIT_TEST_RXN_ARRHENIUS_SRC})
-target_link_libraries(unit_test_rxn_arrhenius camplib)
 
 ######################################################################
 # test_camp_core

Dockerfile.intel

@@ -0,0 +1,78 @@
+FROM intel/oneapi-hpckit:latest
+
+RUN apt update \
+    && apt install -y software-properties-common \
+    && add-apt-repository universe \
+    && apt update \
+    && apt install -y \
+        build-essential \
+        make \
+        libhdf5-dev \
+        libnetcdf-dev \
+        libnetcdff-dev \
+        libmetis-dev \
+        liblapack-dev \
+        libopenblas-dev \
+        libgsl-dev \
+        cmake \
+    && apt clean
+
+# set compilers
+ENV CC=icx
+ENV CXX=icpx
+ENV FC=ifx
+
+# Build the SuiteSparse libraries for sparse matrix support
+# (-k included because of problem with SuiteSparse security certificate - 1 Aug 2021)
+RUN curl -kLO http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.1.0.tar.gz \
+    && tar -zxvf SuiteSparse-5.1.0.tar.gz \
+    && cd SuiteSparse \
+    && make install INSTALL=/usr/local BLAS="-L/lib64 -lopenblas"
+
+# Install json-fortran
+RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/6.1.0.tar.gz \
+    && tar -zxvf 6.1.0.tar.gz \
+    && cd json-fortran-6.1.0 \
+    && mkdir build \
+    && cd build \
+    && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
+    && make install
+
+# copy CVODE source
+COPY cvode-3.4-alpha.tar.gz /cvode-3.4-alpha.tar.gz
+
+# Install a modified version of CVODE
+RUN tar -zxvf /cvode-3.4-alpha.tar.gz \
+    && cd cvode-3.4-alpha \
+    && mkdir build \
+    && cd build \
+    && cmake -D CMAKE_BUILD_TYPE=release \
+             -D CMAKE_C_FLAGS_DEBUG="-g -pg" \
+             -D CMAKE_EXE_LINKER_FLAGS_DEBUG="-pg" \
+             -D CMAKE_MODULE_LINKER_FLAGS_DEBUG="-pg" \
+             -D CMAKE_SHARED_LINKER_FLAGS_DEBUG="-pg" \
+             -D KLU_ENABLE:BOOL=TRUE \
+             -D KLU_LIBRARY_DIR=/usr/local/lib \
+             -D KLU_INCLUDE_DIR=/usr/local/include \
+             .. \
+    && make install
+
+# copy CAMP source code and data
+COPY . /camp
+
+# Update environment variables
+ENV LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/lib:/usr/local/lib64:/usr/local/jsonfortran-gnu-6.1.0/lib"
+ENV PATH="${PATH}:/usr/local/jsonfortran-gnu-6.1.0/lib"
+
+# Build CAMP
+ RUN mkdir build \
+    && cd build \
+    && export JSON_FORTRAN_HOME="/usr/local/jsonfortran-intelllvm-6.1.0" \
+    && cmake -D CMAKE_BUILD_TYPE=release \
+             -D CMAKE_C_FLAGS_DEBUG="-pg" \
+             -D CMAKE_Fortran_FLAGS_DEBUG="-pg" \
+             -D CMAKE_MODULE_LINKER_FLAGS="-pg" \
+             /camp \
+    && make -j install
+
+WORKDIR /build

data/CAMP_v1_paper/binned/camp_monarch_interface.F90

@@ -1213,7 +1213,7 @@ end subroutine do_print
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
   !> Finalize the interface
-  elemental subroutine finalize(this)
+  subroutine finalize(this)
 
     !> PartMC-camp <-> MONARCH interface
     type(monarch_interface_t), intent(inout) :: this

data/CAMP_v1_paper/modal/camp_monarch_interface.F90

@@ -1236,7 +1236,7 @@ end subroutine do_print
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
   !> Finalize the interface
-  elemental subroutine finalize(this)
+  subroutine finalize(this)
 
     !> PartMC-camp <-> MONARCH interface
     type(monarch_interface_t), intent(inout) :: this

src/aero_phase_data.F90

@@ -127,7 +127,7 @@ module camp_aero_phase_data
     !> Print the aerosol phase data
     procedure :: print => do_print
     !> Finalize the aerosol phase data
-    final :: finalize
+    final :: finalize, finalize_array
 
     ! Private functions
     !> Ensure there is enough room in the species dataset to add a specified
@@ -151,7 +151,7 @@ module camp_aero_phase_data
     !> Dereference the pointer
     procedure :: dereference
     !> Finalize the pointer
-    final :: ptr_finalize
+    final :: ptr_finalize, ptr_finalize_array
   end type aero_phase_data_ptr
 
 contains
@@ -584,7 +584,7 @@ end subroutine do_print
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
   !> Finalize the aerosol phase data
-  elemental subroutine finalize(this)
+  subroutine finalize(this)
 
     !> Aerosol phase data
     type(aero_phase_data_t), intent(inout) :: this
@@ -599,6 +599,22 @@ elemental subroutine finalize(this)
 
   end subroutine finalize
 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+  !> Finalize the aerosol phase data
+  subroutine finalize_array(this)
+
+    !> Aerosol phase data
+    type(aero_phase_data_t), intent(inout) :: this(:)
+
+    integer(kind=i_kind) :: i_phase
+
+    do i_phase = 1, size(this)
+      call finalize(this(i_phase))
+    end do
+
+  end subroutine finalize_array
+
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
   !> Ensure there is enough room in the species dataset to add a specified
@@ -685,7 +701,7 @@ end subroutine dereference
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
   !> Finalize a pointer to aerosol phase data
-  elemental subroutine ptr_finalize(this)
+  subroutine ptr_finalize(this)
 
     !> Pointer to aerosol phase data
     type(aero_phase_data_ptr), intent(inout) :: this
@@ -694,6 +710,22 @@ elemental subroutine ptr_finalize(this)
 
   end subroutine ptr_finalize
 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+  !> Finalize an array of pointers to aerosol phase data
+  subroutine ptr_finalize_array(this)
+
+    !> Array of pointers to aerosol phase data
+    type(aero_phase_data_ptr), intent(inout) :: this(:)
+
+    integer(kind=i_kind) :: i_ptr
+
+    do i_ptr = 1, size(this)
+      call ptr_finalize(this(i_ptr))
+    end do
+
+  end subroutine ptr_finalize_array
+
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 #undef NUM_STATE_VAR_

src/aero_rep_data.F90

@@ -145,7 +145,7 @@ module camp_aero_rep_data
     !> Dereference the pointer
     procedure :: dereference
     !> Finalize the pointer
-    final :: ptr_finalize
+    final :: ptr_finalize, ptr_finalize_array
   end type aero_rep_data_ptr
 
   !> Update cookie
@@ -652,7 +652,7 @@ end subroutine dereference
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
   !> Finalize a pointer to an aerosol representation
-  elemental subroutine ptr_finalize(this)
+  subroutine ptr_finalize(this)
 
     !> Pointer to an aerosol representation
     type(aero_rep_data_ptr), intent(inout) :: this
@@ -661,6 +661,22 @@ elemental subroutine ptr_finalize(this)
 
   end subroutine ptr_finalize
 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+  !> Finalize an array of pointers to aerosol representations
+  subroutine ptr_finalize_array(this)
+
+    !> Array of pointers to aerosol representations
+    type(aero_rep_data_ptr), intent(inout) :: this(:)
+
+    integer(kind=i_kind) :: i
+
+    do i = 1, size(this)
+      call ptr_finalize(this(i))
+    end do
+
+  end subroutine ptr_finalize_array
+
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
   !> Get the update data aerosol representation type